WASHINGTON — Matthew G. Whitaker, the attorney general’s chief of staff, jockeyed over the last two months to replace his boss by forging a close relationship with the White House, where he was seen as a reliable political ally. On Wednesday, President Trump fired Jeff Sessions and named Mr. Whitaker acting attorney general, rewarding his loyalty.

Inside the Justice Department, senior officials, including Rod J. Rosenstein, the deputy attorney general, have viewed Mr. Whitaker with intense suspicion. Before his current job at the Justice Department, Mr. Whitaker, a former college football tight end, was openly hostile on television and social media toward the special counsel, Robert S. Mueller III, and was seen by department officials as a partisan and a White House spy.

The special counsel is leading the investigation into whether any of Mr. Trump’s associates conspired with Russia during 2016 election and whether the president tried to obstruct the inquiry. Now Mr. Whitaker will oversee Mr. Mueller’s investigation, prompting concerns that he could move swiftly to shut it down or hobble it, despite serious questions about his own potential conflicts in supervising it.

In August 2017, Mr. Whitaker highlighted on Twitter a Philly.com opinion article with the headline “Note to Trump’s Lawyer: Do Not Cooperate With Mueller Lynch Mob.” In his tweet, Mr. Whitaker wrote that it was “worth a read.”

The same day, as a legal commentator for CNN, he wrote an opinion article for the cable network’s website with the headline “Mueller’s Investigation of Trump Is Going Too Far.” He called on Mr. Rosenstein to “order Mueller to limit the scope of his investigation.”

In another tweet that same summer, Mr. Whitaker argued against legislation that would protect Mr. Mueller’s investigation and accused the F.B.I. of intimidation tactics when agents raided the house of Paul Manafort, the president’s former campaign chairman. Mr. Manafort was prosecuted by Mr. Mueller’s team and later convicted of federal charges.

Mr. Whitaker and Mr. Trump also share similar views on what they consider the need for a special counsel to investigate Hillary Clinton’s use of a private email server. The F.B.I. investigated but closed the case without bringing charges in 2016. Mr. Sessions rebuffed calls for another special counsel.

“Whitaker’s appointment raises blaring alarms about the acceleration of obstruction of justice and a fundamental attack on the rule of law in our country,” Senator Ron Wyden of Oregon, a Democrat on the Senate Intelligence Committee, said in a statement. “Congress must act right now to protect the special counsel’s investigation.”

People close to the president said Mr. Whitaker first came to the attention of Mr. Trump because he liked watching Mr. Whitaker express skepticism about aspects of Mr. Mueller’s investigation on television.

Image

Mr. Whitaker’s Twitter page, where he has argued against legislation that would protect the special counsel’s investigation.Creditvia Twitter

In August 2017, Mr. Whitaker appeared on CNN and said that if Mr. Mueller began investigating the Trump Organization, “I think that would be crossing the red line.”

In a CNN interview the month before, Mr. Whitaker offered a situation in which Mr. Trump could try to hobble Mr. Mueller’s investigation behind the scenes by pressuring the Justice Department to cut the special counsel’s budget.

He said that situation was “a little more stage-crafty than the blunt instrument of firing the attorney general and trying to replace him.”

The burly Mr. Whitaker, 49, whose Twitter profile shows him lifting heavy weights, played football for the University of Iowa Hawkeyes. He played in the 1991 Rose Bowl, where he caught a nine-yard pass, which he said in a 2015 interview was “one of the greatest experiences I ever had as a Hawkeye.” He graduated in 1992 and had once considered moving to Hollywood to make his fortune.

Instead he attended the University of Iowa College of Law. In 2004, he was appointed to be United States attorney for the Southern District of Iowa, a position he held until 2009. He then ran for Senate in 2014, when he campaigned on repealing the Affordable Care Act.

After losing the Republican primary to Senator Joni Ernst, Mr. Whitaker became involved in a shadowy business venture in October 2014, joining the advisory board of World Patent Marketing Inc., in Miami Beach, as a paid member. The company charged people thousands of dollars for the service of helping them patent an invention and promote it, but the Federal Trade Commission accused the enterprise last year of cheating people of nearly $26 million. The suit, first reported by Miami New Times, was settled this May, when the company’s chief executive agreed to discontinue the service in question.

During Mr. Whitaker’s tenure, the group called for investigations into, among others, Senator Evan Bayh of Indiana, Representative Patrick E. Murphy of Florida and Representative Ted Strickland of Ohio, all Democrats who ran for Senate in 2016.

When President Barack Obama nominated Judge Merrick B. Garland to the Supreme Court, Mr. Whitaker’s group demanded that Harvard University release records related to Judge Garland’s position in debates there as an undergraduate in 1973 over whether to allow R.O.T.C. recruiters on campus.

Mr. Whitaker has been open about linking religion with legal judgments. In 2014, while running for the Senate in Iowa, Mr. Whitaker said in a debate that he wanted to examine the “worldview” of judges or potential judges: “Are they people of faith? Do they have a biblical view of justice?”

“If they have a secular worldview, where this is all we have here on Earth, then I’m going to be very concerned about that judge,” Mr. Whitaker said.

Mr. Whitaker has been focused on Mrs. Clinton for years, and denounced her publicly in his role as executive director of FACT. In March 2016, he wrote an op-ed article for The Hill that argued that Obama administration officials needed to appoint a special counsel to investigate Mrs. Clinton’s use of a private email server while working as secretary of state.

“Perhaps the need for special counsel would not be as clear and urgent without the troubling track record Clinton has had with the truth in this matter,” he wrote.

In May 2017, Mr. Whitaker wrote an op-ed for The Hill in which he praised Mr. Trump’s decision to fire James B. Comey, the F.B.I. director. He said he disagreed with Mr. Comey’s assessment that “no reasonable prosecutor” would have brought a criminal case against Mrs. Clinton.

It is not clear whether the president intends to nominate Mr. Whitaker to be the next attorney general, or whether he will choose someone of greater stature and experience. But Mr. Whitaker has the support of Senator Charles E. Grassley, the Iowa Republican who is chairman of the Senate Judiciary Committee. Mr. Grassley supported Mr. Whitaker to be appointed United States attorney in Iowa in 2004 and was pleased with the decision on Wednesday to name him acting attorney general.

“I look forward to working with Matt Whitaker as he takes the helm of the Justice Department,” Mr. Grassley said in a statement. “A fellow Iowan, who I’ve known for many years, Matt will work hard and make us proud. The Justice Department is in good hands during this time of transition.”

It is likely that Mr. Whitaker will be in the position until at least early next year because the Senate legislative calendar would make it nearly impossible to confirm a new attorney general before the current term ends in December.

Mr. Whitaker’s rise comes after a New York Times article disclosed in September that Mr. Rosenstein had discussed secretly taping his conversations with the president and talked about using the 25th Amendment to remove Mr. Trump from office.

Earlier versions of this article incorrectly identified a member of Congress who was scrutinized by the Foundation for Accountability and Civic Trust. It was Representative Patrick E. Murphy of Florida, not Senator Christopher S. Murphy of Connecticut.

Correction:Nov. 8, 2018

Earlier versions of this article misidentified the game at which Matthew G. Whitaker caught a touchdown pass on a faked field goal. It was at a November 1990 game against Illinois, not at the 1991 Rose Bowl.

A version of this article appears in print on , on Page A14 of the New York edition with the headline: Partisan Appointee Has Voiced Doubts About the Mueller Investigation. Order Reprints | Today’s Paper | Subscribe